naked-singularity-v0.1.2 :: updated tensorflow-cpu.def and

tensorflow-gpu.def on comet to build both python(2) and python3 versions side-by-side; also added many of the more common python-based data science and machine learning packages

naked-singularity-v0.1.2 :: updated tensorflow-cpu.def and

tensorflow-gpu.def on comet to build both python(2) and python3 versions side-by-side; also added many of the more common python-based data science and machine learning packages
naked-singularity-v0.1.2 :: updated tensorflow-cpu.def and
01608da5 · Marty Kandes · 8e5ea3fc · 01608da5 · 01608da5 · 01608da5
Commit 01608da5 authored Feb 16, 2018 by Marty Kandes
--- a/README
+++ b/README
@@ -10,8 +10,6 @@ DESCRIPTION

    * http://singularity.lbl.gov/

-USAGE
-
 STATUS

    A work in progress. 
@@ -29,6 +27,10 @@ AUTHOR
    HPC User Services Group, San Diego Supercomputer Center
    University of California, San Diego

+VERSION
+
+    0.1.2
+
 LAST UPDATED

-    Thursday, December 20th, 2017
+    Wednesday, February 14th, 2018
--- a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-cpu.def
@@ -8,12 +8,11 @@ OSVersion: xenial
    AUTHOR_EMAIL mkandes@sdsc.edu
    APPLICATION_NAME tensorflow
    APPLICATION_VERSION 1.4
-    APPLICATION_URL https://www.tensorflow.org/
+    APPLICATION_URL https://www.tensorflow.org
    SYSTEM_NAME comet
    SYSTEM_SINGULARITY_VERSION 2.3.2
    SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-    VERSION 0.0.6
-    LAST_UPDATED 20180108
+    LAST_UPDATED 20180214

 %setup

@@ -48,29 +47,51 @@ OSVersion: xenial

    apt-get -y update && apt-get -y upgrade

+    # Install common packages from 'main'
+    apt-get -y install autoconf
+    apt-get -y install automake
+    apt-get -y install build-essential
+    apt-get -y install libtool
+    apt-get -y install pkg-config
+    apt-get -y install gfortran
+    apt-get -y install zip
+
+    # Make filesystem mount points
    mkdir /cvmfs /oasis /projects /scratch

-    #echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
-    #curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+    # Build and install from source in /opt
+    cd /opt
+
+    ### Install Bazel using custom APT repository
+    ###apt-get -y install openjdk-8-jdk
+    ###echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
+    ###curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+    ###apt-get -y update
+    ###apt-get -y install bazel
+    ###apt-get -y upgrade bazel

-    apt-get -y update
+    # Install Bazel from Debian Package
    apt-get -y install openjdk-8-jdk
-    #apt-get -y install bazel
+    apt-get -y install zlib1g-dev
+    wget https://github.com/bazelbuild/bazel/releases/download/0.8.1/bazel_0.8.1-linux-x86_64.deb
+    dpkg -i bazel_0.8.1-linux-x86_64.deb
+    rm bazel_0.8.1-linux-x86_64.deb
+
+    # Install expect to automate responses to TensorFlow build questions
    apt-get -y install expect
+
+    # Install TensorFlow python dependencies
    apt-get -y install python-numpy
    apt-get -y install python-dev
    apt-get -y install python-pip
    apt-get -y install python-wheel
-    apt-get -y install zlib1g-dev
-
-    wget https://github.com/bazelbuild/bazel/releases/download/0.8.1/bazel_0.8.1-linux-x86_64.deb
-    dpkg -i bazel_0.8.1-linux-x86_64.deb
    
-    cd /opt
+    # Download TensorFlow source
    git clone https://github.com/tensorflow/tensorflow 
    cd /opt/tensorflow
    git checkout r1.4

+    # Build TensorFlow for python(2)
    echo '#!/usr/bin/expect -f' > configure.exp
    echo 'spawn ./configure' >> configure.exp
    echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
@@ -108,8 +129,84 @@ OSVersion: xenial
    bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg

    pip install /opt/tensorflow_pkg/tensorflow-1.4.1-cp27-cp27mu-linux_x86_64.whl
+    rm -rf /opt/tensorflow_pkg
+    rm configure.exp
+
+    # Install TensorFlow python3 dependencies
+    apt-get -y install python3-numpy
+    apt-get -y install python3-dev
+    apt-get -y install python3-pip
+    apt-get -y install python3-wheel
+
+    # Build TensorFlow for python3 
+    echo '#!/usr/bin/expect -f' > configure.exp
+    echo 'spawn ./configure' >> configure.exp
+    echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
+    echo 'send "/usr/bin/python3\r"' >> configure.exp
+    echo 'expect "Please input the desired Python library path to use.  Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> configure.exp
+    echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> configure.exp
+    echo 'send "Y\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with OpenCL support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect ": "' >> configure.exp
+    echo 'send " -march=native\r"' >> configure.exp
+    echo 'expect "> "' >> configure.exp
+
+    chmod +x configure.exp
+    ./configure.exp
+
+    bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
+    bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg
+
+    pip3 install /opt/tensorflow_pkg/tensorflow-1.4.1-cp35-cp35m-linux_x86_64.whl
+    rm -rf /opt/tensorflow_pkg
+    rm configure.exp

+    # Install common python and python3 packages for data science and 
+    # machine learning applications
    apt-get -y install python-scipy
+    apt-get -y install python-pandas
+    apt-get -y install python-matplotlib
+    apt-get -y install ipython
+    apt-get -y install ipython-notebook
+    apt-get -y install python-sympy
+    apt-get -y install python-nose
+    apt-get -y install python-sklearn
+    apt-get -y install python-mlpy
+    apt-get -y install python-nltk
+    apt-get -y install python-statsmodels
+    apt-get -y install libopencv-dev 
+    apt-get -y install python-opencv
+
+    apt-get -y install python3-scipy
+    apt-get -y install python3-pandas
+    apt-get -y install python3-matplotlib
+    apt-get -y install ipython3
+    apt-get -y install ipython3-notebook
+    apt-get -y install python3-sympy
+    apt-get -y install python3-nose
+    apt-get -y install python3-sklearn
+    apt-get -y install python3-nltk
+
+    # Update database for mlocate
+    updatedb

 %files

@@ -118,4 +215,5 @@ OSVersion: xenial
 %test

    time -p python /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
+    time -p python3 /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py

--- a/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def
+++ b/definition-files/us/ucsd/sdsc/comet/tensorflow/tensorflow-gpu.def
@@ -8,12 +8,11 @@ OSVersion: xenial
    AUTHOR_EMAIL mkandes@sdsc.edu
    APPLICATION_NAME tensorflow
    APPLICATION_VERSION 1.4
-    APPLICATION_URL https://www.tensorflow.org/
+    APPLICATION_URL https://www.tensorflow.org
    SYSTEM_NAME comet
    SYSTEM_SINGULARITY_VERSION 2.3.2
    SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html 
-    VERSION 0.0.5
-    LAST_UPDATED 20180108
+    LAST_UPDATED 20180214

 %setup

@@ -48,12 +47,24 @@ OSVersion: xenial

    apt-get -y update && apt-get -y upgrade

+    # Install common packages from 'main'
+    apt-get -y install autoconf
+    apt-get -y install automake
+    apt-get -y install build-essential
+    apt-get -y install libtool
+    apt-get -y install pkg-config
+    apt-get -y install gfortran
+    apt-get -y install zip
+
+    # Make filesystem mount points
    mkdir /cvmfs /oasis /projects /scratch

+    # Location of NVIDIA repositories
    declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
    declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
    declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"

+    # Install NVIDIA package dependencies
    apt-get -y install x11-common
    apt-get -y install xserver-xorg-core
    apt-get -y install cmake
@@ -87,6 +98,7 @@ OSVersion: xenial

    cd /opt

+    # Download NVIDIA drivers, libraries, and packages
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb" 
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
@@ -134,6 +146,7 @@ OSVersion: xenial
    wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
    wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"

+    # Install NVIDIA drivers, libraries, and packages
    dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
    dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
    dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
@@ -181,31 +194,109 @@ OSVersion: xenial
    dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
    dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb

+    rm *.deb
+
+    # Set paths to CUDA binaries and libraries
    export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
    export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"

-    #echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
-    #curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+    # Build and install from source in /opt
+    cd /opt
+
+    ### Install Bazel using custom APT repository
+    ###apt-get -y install openjdk-8-jdk
+    ###echo "deb [arch=amd64] http://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
+    ###curl https://bazel.build/bazel-release.pub.gpg | apt-key add -
+    ###apt-get -y update
+    ###apt-get -y install bazel
+    ###apt-get -y upgrade bazel

-    apt-get -y update
+    # Install Bazel from Debian Package
    apt-get -y install openjdk-8-jdk
-    #apt-get -y install bazel
-    apt-get -y install expect
-    apt-get -y install python-dev
-    apt-get -y install python3-numpy 
-    apt-get -y install python3-dev 
-    apt-get -y install python3-pip 
-    apt-get -y install python3-wheel
-    apt-get -y install libcupti-dev
    apt-get -y install zlib1g-dev
-
    wget https://github.com/bazelbuild/bazel/releases/download/0.8.1/bazel_0.8.1-linux-x86_64.deb
    dpkg -i bazel_0.8.1-linux-x86_64.deb
+    rm bazel_0.8.1-linux-x86_64.deb

+    # Install expect to automate responses to TensorFlow build questions
+    apt-get -y install expect
+
+    # Install TensorFlow python dependencies
+    apt-get -y install python-numpy
+    apt-get -y install python-dev
+    apt-get -y install python-pip
+    apt-get -y install python-wheel
+
+    # Download TensorFlow source
    git clone https://github.com/tensorflow/tensorflow
-    cd tensorflow
+    cd /opt/tensorflow
    git checkout r1.4

+    # Build TensorFlow for python(2)
+    echo '#!/usr/bin/expect -f' > configure.exp
+    echo 'spawn ./configure' >> configure.exp
+    echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
+    echo 'send "/usr/bin/python\r"' >> configure.exp
+    echo 'expect "Please input the desired Python library path to use.  Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> configure.exp
+    echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> configure.exp
+    echo 'send "Y\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with OpenCL support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> configure.exp
+    echo 'send "Y\r"' >> configure.exp
+    echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 8.0\]: "' >> configure.exp
+    echo 'send "8.0\r"' >> configure.exp
+    echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> configure.exp
+    echo 'send "/usr/local/cuda\r"' >> configure.exp
+    echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 6.0\]: "' >> configure.exp
+    echo 'send "6.0.21\r"' >> configure.exp
+    echo 'expect "Please specify the location where cuDNN 6.0.21 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> configure.exp
+    echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> configure.exp
+    echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> configure.exp
+    echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> configure.exp
+    echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> configure.exp
+    echo 'send "3.7,6.0\r"' >> configure.exp
+    echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> configure.exp
+    echo 'send "/usr/bin/gcc\r"' >> configure.exp
+    echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> configure.exp
+    echo 'send "N\r"' >> configure.exp
+    echo 'expect ": "' >> configure.exp
+    echo 'send " -march=native\r"' >> configure.exp
+    echo 'expect "> "' >> configure.exp
+
+    chmod +x configure.exp
+    ./configure.exp
+
+    bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
+    bazel-bin/tensorflow/tools/pip_package/build_pip_package /opt/tensorflow_pkg
+
+    pip install /opt/tensorflow_pkg/tensorflow-1.4.1-cp27-cp27mu-linux_x86_64.whl
+
+    rm -rf /opt/tensorflow_pkg
+    rm configure.exp
+
+    # Install TensorFlow python3 dependencies
+    apt-get -y install python3-numpy
+    apt-get -y install python3-dev
+    apt-get -y install python3-pip
+    apt-get -y install python3-wheel
+
+    # Build TensorFlow for python3
    echo '#!/usr/bin/expect -f' > configure.exp
    echo 'spawn ./configure' >> configure.exp
    echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> configure.exp
@@ -260,7 +351,37 @@ OSVersion: xenial

    pip3 install /opt/tensorflow_pkg/tensorflow-1.4.1-cp35-cp35m-linux_x86_64.whl

+    rm -rf /opt/tensorflow_pkg
+    rm configure.exp
+
+    # Install common python and python3 packages for data science and
+    # machine learning applications
+    apt-get -y install python-scipy
+    apt-get -y install python-pandas
+    apt-get -y install python-matplotlib
+    apt-get -y install ipython
+    apt-get -y install ipython-notebook
+    apt-get -y install python-sympy
+    apt-get -y install python-nose
+    apt-get -y install python-sklearn
+    apt-get -y install python-mlpy
+    apt-get -y install python-nltk
+    apt-get -y install python-statsmodels
+    apt-get -y install libopencv-dev
+    apt-get -y install python-opencv
+
    apt-get -y install python3-scipy
+    apt-get -y install python3-pandas
+    apt-get -y install python3-matplotlib
+    apt-get -y install ipython3
+    apt-get -y install ipython3-notebook
+    apt-get -y install python3-sympy
+    apt-get -y install python3-nose
+    apt-get -y install python3-sklearn
+    apt-get -y install python3-nltk
+
+    # Update database for mlocate
+    updatedb

 %files

@@ -268,4 +389,7 @@ OSVersion: xenial

 %test

+    # Test TensorFlow for both python and python3
+    time -p python /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
    time -p python3 /opt/tensorflow/tensorflow/examples/tutorials/mnist/mnist_deep.py
+
--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
@@ -11,10 +11,9 @@ OSVersion: xenial
    APPLICATION_URL https://developer.nvidia.com/cuda-zone
    DEVICE_DRIVER_VERSION 367.48
    SYSTEM_NAME comet
-    SYSTEM_SINGULARITY_VERSION 2.3.1
+    SYSTEM_SINGULARITY_VERSION 2.3.2
    SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html 
-    VERSION 0.0.2
-    LAST_UPDATED 20170831
+    LAST_UPDATED 20180214

 %setup

@@ -49,12 +48,24 @@ OSVersion: xenial

    apt-get -y update && apt-get -y upgrade

+    # Install common packages from 'main'
+    apt-get -y install autoconf
+    apt-get -y install automake
+    apt-get -y install build-essential
+    apt-get -y install libtool
+    apt-get -y install pkg-config
+    apt-get -y install gfortran
+    apt-get -y install zip
+
+    # Make filesystem mount points
    mkdir /cvmfs /oasis /projects /scratch

+    # Location of NVIDIA repositories
    declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
    declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
    declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"

+    # Install NVIDIA package dependencies
    apt-get -y install x11-common
    apt-get -y install xserver-xorg-core
    apt-get -y install cmake
@@ -88,6 +99,7 @@ OSVersion: xenial

    cd /opt

+    # Download NVIDIA drivers, libraries, and packages
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb" 
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
    wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
@@ -129,12 +141,13 @@ OSVersion: xenial
    wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
    wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"

-    wget --wait=10 "${ML_REPO_URL}/libcudnn5_5.1.10-1+cuda8.0_amd64.deb"
-    wget --wait=10 "${ML_REPO_URL}/libcudnn5-dev_5.1.10-1+cuda8.0_amd64.deb"
+    wget --wait=10 "${ML_REPO_URL}/libcudnn6_6.0.21-1+cuda8.0_amd64.deb"
+    wget --wait=10 "${ML_REPO_URL}/libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb"

-    wget --wait=10 "${ML_REPO_URL}/libnccl1_1.2.3-1+cuda8.0_amd64.deb"
-    wget --wait=10 "${ML_REPO_URL}/libnccl-dev_1.2.3-1+cuda8.0_amd64.deb"
+    wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
+    wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"

+    # Install NVIDIA drivers, libraries, and packages
    dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
    dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
    dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
@@ -176,21 +189,28 @@ OSVersion: xenial
    dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
    dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb

-    dpkg -i libcudnn5_5.1.10-1+cuda8.0_amd64.deb
-    dpkg -i libcudnn5-dev_5.1.10-1+cuda8.0_amd64.deb 
+    dpkg -i libcudnn6_6.0.21-1+cuda8.0_amd64.deb
+    dpkg -i libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb

-    dpkg -i libnccl1_1.2.3-1+cuda8.0_amd64.deb
-    dpkg -i libnccl-dev_1.2.3-1+cuda8.0_amd64.deb 
+    dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
+    dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb

+    rm *.deb
+
+    # Set paths to CUDA binaries and libraries
    export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
    export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"

+    # Update database for mlocate
+    updatedb
+
 %files

 %runscript

 %test

+    # Test if nvcc was installed properly
    export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
    export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
    nvcc --version

--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
@@ -10,10 +10,9 @@ OSVersion: xenial
    APPLICATION_VERSION none
    APPLICATION_URL none
    SYSTEM_NAME comet
-    SYSTEM_SINGULARITY_VERSION 2.3.1
+    SYSTEM_SINGULARITY_VERSION 2.3.2
    SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-    VERSION 0.0.5
-    LAST_UPDATED 20170811
+    LAST_UPDATED 20180213

 %setup

@@ -48,8 +47,24 @@ OSVersion: xenial

    apt-get -y update && apt-get -y upgrade

+    # Install common packages from 'main'
+    apt-get -y install autoconf
+    apt-get -y install automake
+    apt-get -y install build-essential
+    apt-get -y install libtool
+    apt-get -y install pkg-config
+    apt-get -y install gfortran
+    apt-get -y install zip
+
+    # Make filesystem mount points
    mkdir /cvmfs /oasis /projects /scratch

+    # Build and install from souce in /opt
+    cd /opt
+
+    # Update database for mlocate
+    updatedb 
+
 %files

 %runscript